1. CIS 401: Applied Scientific Computing with MATLAB Andrew Pershing 3134 Snee Hall ajp9@cornell.edu 255-5552

2. Outline Course Description Details Policies Intro to CIS Tools Curriculum Role of Computing in Science and Engineering Basic Concepts

3. Course Goals This course will: –Introduce the basic functionality of MATLAB –Demonstrate its utility in scientific research –Identify interesting concepts and useful techniques in scientific computing By the end of the course, you should have the skills necessary to apply MATLAB to your research and learn how to extend its capabilities

4. Syllabus 1. Course intro and basic concepts 2.Intro to Matlab: the workspace 3.Matlab fundamentals: arrays, & simple plots 4.Matlab programming: loops and conditionals 5.Text processing and a survey of Matlab 6.Improving performance 7.Statistics and simple plots 8.Applied Scientific Computing I: Simulation 9.Applied Scientific Computing II: ODE/Optimization 10.File I/0 11.Applied Scientific Computing III: Linear systems 12.Class projects

5. Course Ungoals This course will NOT: –Teach you how to program (try CS 100m) You should be comfortable writing programs in some language and be familiar with the following concepts: –Programs vs. algorithms –Iteration –Conditionals and logic –Recursion –Subroutines, variables, and scope –Teach you numerical methods (CS 322,421, 62X) –Cover everything in MATLAB

6. http://www.cs.cornell.edu/Courses/cs401/2003sp –Contains syllabus, lecture notes, examples, homework Office Hours –Tuesday & Wednesday, 3-4 in 3134 Snee (or by appointment) Registration: CIS 401 or COM S 401 –get my signature or CS Undergrad office (303 Upson) –Number:641-522 –S/U only, 1 credit –Last day to add/drop: Monday, September 8 ! Course Business:

7. Requirements Reference Text: Hanselman and Littlefield Mastering Matlab 6 –No required reading, but this is a great reference Find a computer with MATLAB: –Check departmental labs--good site licensing for Cornell machines http://www.cit.cornell.edu/software/licenses/matlab.html –ACCEL in Carpenter Hall –Upson, Carpenter, and Dickson Labs –Buy student version

8. 4 assignments: 1 per week, due Wednesday, 5PM by e-mail If you complete each assignment on time and demonstrate a basic command of the material, you will pass! Course policies are strict: –A direct consequence of the “mini-course” format This course operates as a contract between you and me Course Policies

9. I agree to: –Begin and end lecture on time –Put lecture notes on website prior to lecture (usually night before) –Be available during office hours –Make the assignments of reasonable length (2-4 hours) focusing on material from lectures The Contract

10. Assignments Assignments will be fairly short –“Essential Knowledge” short answer questions from lecture material –A programming task opportunity to apply Matlab Problem Set 4 will be special –You will have to come up with a programming task, relevant to your area of expertise –Proposals will be due with PS3, code with PS4 –Brief presentation on last day

11. By registering for the course, you agree to: –Arrive on time –Participate in the course by asking questions and coming to office hours –Turn in your assignments on time Late work will not be accepted and will jeopardize you chance of passing! The only exceptions are for documented, university- sanctioned reasons such as severe illness or by prior arrangement made w/ me 3 days before (includes religious holidays, sports, etc.) The Contract

12. –Cornell University has recognized that computing and information science has emerged as a key enabling discipline vital to nearly all of its scholarly and scientific pursuits. –The Faculty of Computing and Information is founded on the recognition that the ideas and technology of computing and information science are relevant to every academic discipline. –We are united in the need to bring together a core of faculty in this field from across the traditional colleges. CIS and FCI

13. CIS 401 is the first in a series of courses designed to teach “applied scientific computing” CIS Tools Curriculum CS Science & Engineering Scientific computing pure applied

14. CIS Tools Curriculum “Pure” Scientific Computing –Focus is on algorithms for general problems such as optimization, linear systems, differential equations –Concerned with accuracy, stability, and efficiency of these algorithms “Applied” Scientific Computing –How to apply general algorithms to solve scientific problems –Algorithms are “black boxes” that we string together to get our work done –Applied SC is also concerned with data

15. CIS Tools Curriculum Fall: MATLAB –401: the basics –402: visualization (starts September 30) Spring: General tools –403: Developing scientific computer programs (compilers, debuggers, managing large projects, designing programs) –404: Numerical libraries (compiling and linking, static vs. dynamic libraries, BLAS, LAPACK, MPI)

16. Role of Computing in Science and Engineering Scientists have been computing for centuries, well before digital computers Digital computers allow us to do thing faster, but often the ideas are ancient Example: Velocity from pressure data

17. Geostrophy Measuring the velocity of atmosphere and ocean is difficult, but observing pressure is easy Fortunately, velocity can be determined from pressure using the geostrophic relationship: Pressure gradient = Coriolis force (Earth’s rotation)

18. Geostrophy An alternative to pressure is sea- surface height SSH can be measured by satellites

19. Geostrophy Use hydrostatic equation: to introduce SSH (Z) into geostrophic equation:

20. Geostrophy in MATLAB MATLAB allows us to compute the velocity: in only a few lines Can examine results graphically

21. So, what’s the point? Theme of the FCI is that computing is general The geostropic calculations are a specific instance of the general scientific computing process.

22. Scientific Computing Process It is possible to do all of these things in Matlab, and most of them are easier. DataProgramOutput Currents SSHGeostropic eq.U,V,plot Weather T,V,MFinite diff.T,V,M in future Bioinfomatics ATCGCGTA…Search for genesLocation of genes Electronics SignalFFTPlot of spectrum Economics Historic Stock PricesTrading StrategyMoney Made/Lost

23. Computer Science Review What is a computer? –Program is a series of instructions that tell the processor how to manipulate system read/write to memory, disk calculate CPU Control Unit Arith./Logic Unit Registers L1 cache L2 cache Memory (RAM) Disk Bus

24. Basic Concepts Algorithm vs. Program –A program is a series of commands on a computer –An algorithm is a step-by-step procedure to compute something A program should be an algorithm An algorithm does not require a computer –Ex: To get to my office, 1) Stand up and leave this room 2) Walk west to stairs 3) Go down stairs to door 4) Turn left, then down stairs to left 5) Cross parking lot to right & enter Snee Hall 6) Go up two flights of stairs to 3rd floor 7) Turn left out of stairway, my office is first on left

25. Basic Concepts Programs are constructed from subroutines (or classes or functions) Subroutines are constructed from –variables--name given to a specific region of memory –commands--instructions that change value of variables SSHvel [lat,lon,Z]=SSHdata [U,V]=Geostroph(lat,lon,Z ) MATLAB core language Built-in functions SSHdata read data file parse into lat, lon, Z Geostroph convert lat/lon to distance U,V from geostrophic eq.

26. Variables have a name have value (numeric, text) have type (integer, floating point, char, etc.) Variables can also be data structures (arrays, structs) –Arrays: group of data that can be accessed through subscripts –Ex: primes is an array of 5 prime numbers 1 2 3 5 7 primes primes 1 primes 3 primes 5

27. Commands Simplest command is assignment –a=1; %value of a is 1 after this statement –b=2+a; %value of b is constructed from a –a=2; %changes value of a, what is value of b? Control (if-then-else) or iteration (for, while) Call another subroutine

28. Commands Programming languages differ in syntax –syntax=how commands are written –Java: for(int j=0;j<n;j++){ //code } –Matlab: for j=1:n; %code; end But, all programming languages do the same thing –If you know one language, you can understand programs written in most others.

29. Developing programs Problem: you have a task you want your computer to do, and you need to develop a program to perform it Several approaches, iterative refinement is a simple and effective technique 1. Describe--what will your program/subroutine do? 2. Divide--what are the essential tasks? 3. Repeat--subdivide tasks if possible. The idea is to move from some description of the task (English, math, pictures) to a series of commands

30. Iterative Refinement I.Do Laundry A.Wash B.Dry C.Fold

31. A.Wash 1.Get clothes 2.Place in washer 3.Configure washer 4.Start B.Dry 1.Move from washer to dryer 2.Configure dryer 3.Start C.Fold 1.Remove from dryer 2.If (shirt) then a. Fold shirt else b. Fold pants Do Laundry

32. Main Point of Design –Think before you code!